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Lexical Tools Briefing

Lexical Tools Briefing. The Lexical Systems Group NLM . LHNCBC . CGSB May, 2006. Table of Contents. Introduction Lvg Norm LuiNorm Application Example Users Annual Release Cycle Tests Questions. Introduction – Lexical Tools. Lexical Tools. A suite of text utilities.

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Lexical Tools Briefing

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  1. Lexical Tools Briefing The Lexical Systems Group NLM. LHNCBC. CGSB May, 2006

  2. Table of Contents • Introduction • Lvg • Norm • LuiNorm • Application Example • Users • Annual Release Cycle • Tests • Questions

  3. Introduction – Lexical Tools Lexical Tools • A suite of text utilities

  4. Introduction – Lexical Tools Input Lexical Tools • A suite of text utilities take the given input

  5. Output… Output.3 Input Lexical Tools Output.2 Output.1 Introduction – Lexical Tools • A suite of text utilities that generate, mutate, and filter out lexical variants from the given input

  6. Four Tools Output… Lvg Norm LuiNorm WordIndex Output.3 Input Output.2 Output.1

  7. Tool Types • Command line tools • lvg (Lexical Variants Generation) • norm • luiNorm • wordInd • Lexical Gui Tool (lgt) • Web Tools • Java API’s

  8. Functions • Used in nature language processing for • aggressive text pattern matching • creating normalized and expanded terms • making word, term, phrase indexes • matching queries with indexed entries • increasing recall and/or precision

  9. Facts • Release annually • 100% Java (since 2002) • Free distributed with open source code • Run on different platforms • One complete package • Documents & support

  10. Lexical Variants Generation Lexical Variants Generation

  11. LVG • 58 flow components • 37 options • input filter options (3) • global behavior options (13) • flow specific options (2) • output filter options (19)

  12. Flow Components leave leaves leave inflect leaving left

  13. Command Line Tool > lvg –f:i leave leave|leave|128|1|i|1| leave|leave|128|512|i|1| leave|leaves|128|8|i|1| leave|left|1024|64|i|1| leave|left|1024|32|i|1| leave|leave|1024|1|i|1| leave|leave|1024|262144|i|1| leave|leave|1024|1024|i|1| leave|leaves|1024|128|i|1| leave|leaving|1024|16|i|1|

  14. Fielded Output > lvg –f:i leave 1 leave leave i 1 128 | | | | | Inflections Input Term Flow history Output Term Flow Number Categories

  15. A Serial Flow lowercase Strip diacritics Input term Output term Remove possessive Remove stop words Strip punctuation Word order sort • Flow components can be arranged so that the output of one is the input to another.

  16. A Serial Flow - Example > lvg –f:l:q:g:t:p:w The Gougerot-Sjögren's Syndrome The Gougerot-Sjögren's Syndrome| gougerotsjogren syndrome|2047| 16777215|l+q+g+t+p+w|1|

  17. Parallel Flows Output term noOperation Input term Uninflect Output terms synonyms • Multiple flows can be defined

  18. Parallel Flows - Example > lvg –f:n –f:B:y ear ear|ear|2047|1048575|n|1| ear|aural|1|1|B+y|2| ear|auricularis|1|1|B+y|2| ear|otic|1|1|B+y|2| ear|otor|1|1|B+y|2|

  19. Input Filter Options Output terms Input term Take field 7 from the input > lvg -f:u -t:7 -F:8:6 C0035440|ENG|S|L0035434|VW|S0003894| Rheumatic carditis, acute acute Rheumatic carditis|S0003894

  20. Global Behavior Options Output terms Input term Output terms > lvg -f:L –f:E –s:”\” otitis otitis\otitis\128\513\L\1 otitis\E0044452\128\513\E\2 Change separator to “\”

  21. Input term Output terms Output Filter Options > lvg -f:L -SC -SI hot hot|hot|<adj+verb>|<base+positive+infinitive+pres1p23p>|L|1| Show the category and inflection names

  22. Norm • Composed of 11 Lvg flow components to abstract away from: • case • punctuation • possessive forms • inflections • spelling variants • stop words • diacritics & ligatures • word order

  23. Norm g: remove genitives rs: remove parenthetic plural forms o: replace punctuation with spaces t: strip stop words q: strip diacritics q2: split ligature l: lowercase B: uninflect each words in a term Ct: retrieve citations w: sort words by order q4: get symbol names synonymy

  24. Norm Hodgkin's Diseases, NOS g: remove genitives rs: remove parenthetic plural forms o: replace punctuation with spaces t: strip stop words q: strip diacritics q2: split ligature l: lowercase B: uninflect each words in a term Ct: retrieve citations w: sort words by order q4: get symbol names synonymy

  25. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms o: replace punctuation with spaces t: strip stop words q: strip diacritics q2: split ligature l: lowercase B: uninflect each words in a term Ct: retrieve citations w: sort words by order q4: get symbol names synonymy

  26. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms Hodgkin Diseases, NOS o: replace punctuation with spaces t: strip stop words q: strip diacritics q2: split ligature l: lowercase B: uninflect each words in a term Ct: retrieve citations w: sort words by order q4: get symbol names synonymy

  27. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms Hodgkin Diseases, NOS o: replace punctuation with spaces Hodgkin Diseases NOS t: strip stop words q: strip diacritics q2: split ligature l: lowercase B: uninflect each words in a term Ct: retrieve citations w: sort words by order q4: get symbol names synonymy

  28. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms Hodgkin Diseases, NOS o: replace punctuation with spaces Hodgkin Diseases NOS t: strip stop words Hodgkin Diseases q: strip diacritics q2: split ligature l: lowercase B: uninflect each words in a term Ct: retrieve citations w: sort words by order q4: get symbol names synonymy

  29. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms Hodgkin Diseases, NOS o: replace punctuation with spaces Hodgkin Diseases NOS t: strip stop words Hodgkin Diseases q: strip diacritics Hodgkin Diseases q2: split ligature l: lowercase B: uninflect each words in a term Ct: retrieve citations w: sort words by order q4: get symbol names synonymy

  30. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms Hodgkin Diseases, NOS o: replace punctuation with spaces Hodgkin Diseases NOS t: strip stop words Hodgkin Diseases q: strip diacritics HodgkinDiseases q2: split ligature Hodgkin Diseases l: lowercase B: uninflect each words in a term Ct: retrieve citations w: sort words by order q4: get symbol names synonymy

  31. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms Hodgkin Diseases, NOS o: replace punctuation with spaces Hodgkin Diseases NOS t: strip stop words Hodgkin Diseases q: strip diacritics HodgkinDiseases q2: split ligature Hodgkin Diseases l: lowercase hodgkin diseases B: uninflect each words in a term Ct: retrieve citations w: sort words by order q4: get symbol names synonymy

  32. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms Hodgkin Diseases, NOS o: replace punctuation with spaces Hodgkin Diseases NOS t: strip stop words Hodgkin Diseases q: strip diacritics HodgkinDiseases q2: split ligature Hodgkin Diseases l: lowercase hodgkin diseases B: uninflect each words in a term hodgkin disease Ct: retrieve citations w: sort words by order q4: get symbol names synonymy

  33. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms Hodgkin Diseases, NOS o: replace punctuation with spaces Hodgkin Diseases NOS t: strip stop words Hodgkin Diseases q: strip diacritics HodgkinDiseases q2: split ligature Hodgkin Diseases l: lowercase hodgkin diseases B: uninflect each words in a term hodgkin disease Ct: retrieve citations hodgkin disease w: sort words by order q4: get symbol names synonymy

  34. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms Hodgkin Diseases, NOS o: replace punctuation with spaces Hodgkin Diseases NOS t: strip stop words Hodgkin Diseases q: strip diacritics HodgkinDiseases q2: split ligature Hodgkin Diseases l: lowercase hodgkin diseases B: uninflect each words in a term hodgkin disease Ct: retrieve citations hodgkin disease w: sort words by order disease hodgkin q4: get symbol names synonymy

  35. Norm Hodgkin's Diseases, NOS g: remove genitives Hodgkin Diseases, NOS rs: remove parenthetic plural forms Hodgkin Diseases, NOS o: replace punctuation with spaces Hodgkin Diseases NOS t: strip stop words Hodgkin Diseases q: strip diacritics HodgkinDiseases q2: split ligature Hodgkin Diseases l: lowercase hodgkin diseases B: uninflect each words in a term hodgkin disease Ct: retrieve citations hodgkin disease w: sort words by order disease hodgkin q4: get symbol names synonymy disease hodgkin

  36. Norm: Example • Hodgkin Disease • HODGKINS DISEASE • Hodgkin's Disease • Disease, Hodgkin's • HODGKIN'S DISEASE • Hodgkin's disease • Hodgkins Disease • Hodgkin's disease NOS • Hodgkin's disease, NOS • Disease, Hodgkins • Diseases, Hodgkins • Hodgkins Diseases • Hodgkins disease • hodgkin's disease • Disease;Hodgkins • Disease, Hodgkin disease hodgkin

  37. LuiNorm • A special version of Norm • Used in the UMLS Metathesaurus • Composed of 11 lvg flow components • Replace –f:Ct (in norm) to –f:C • Provide one to one correspondence between an input and an output

  38. LuiNorm g: remove genitives rs: remove parenthetic plural forms o: replace punctuation with spaces t: strip stop words q: strip diacritics q2: split ligature l: lowercase B: uninflect each words in a term C: retrieve canonical form w: sort words by order q4: get symbol names synonymy

  39. Canonical Form • To manage ambiguity generated by uninflection • “left” is uninflected to “left” (adj) or “leave” (verb) • A Canonical class includes terms have same inflections or spelling variants • “left”, “leave”, and “leaf” have same inflections “leaves” • “analog” and “analogue” are spelling variants • Canonical form is an arbitrarily chosen member of a Canonical class • alphabetical order • shortest member • in The SPECIALIST LEXICON

  40. Application Metathesaurus English Strings Normalized string index norm MRXNS.ENG WordInd Normalized word index MRXNW.ENG

  41. Application Normalized string index Normed term norm Query Normalized word index SUIS Metathesaurus Concepts Metathesaurus concepts that match the normalized query

  42. Normed term Query Example Dry Eyes Syndrome norm dry eye syndrome

  43. SUIS Example (Cont.) ENG|dry eye syndrome|C0013238|L0013238|S0004019| ENG|dry eye syndrome|C0013238|L0013238|S0035652| ENG|dry eye syndrome|C0013238|L0013238|S0090228| ENG|dry eye syndrome|C0013238|L0013238|S0090454| ENG|dry eye syndrome|C0013238|L0013238|S0220550| ENG|dry eye syndrome|C0013238|L0013238|S0368350| ENG|dry eye syndrome|C0013238|L0013238|S1459074| Normed term

  44. Example (Cont.) C0013238|ENG|P|L0013238|VS |S0004019|Dry eye syndrome C0013238|ENG|P|L0013238|VS |S0368350|Dry Eye Syndrome C0013238|ENG|P|L0013238|VS |S1459074|dry eye syndrome C0013238|ENG|P|L0013238|VWS|S0090228|Syndrome, Dry Eye C0013238|ENG|P|L0013238|VWS|S0220550|Dry, eye syndrome C0013238|ENG|P|L0013238|VW |S0090454|Syndromes, Dry Eye MRCON SUIS C0013238|ENG|P|L0013238|PF |S0035652| Dry Eye Syndromes

  45. Users • Internal NLM Users • Lexical Systems Group • UMLS Group (Apelon) • MMTX (MetaMap): map text phrases to Metathesaurus concept • UMLS Knowledge Source Server • Clinical Trial • Indexing Initiative • Semantic Knowledge Representation • Terminology Server • Medical Ontology • Word Sense Disambiguation • …

  46. Users (Cont.) • Public Users (USA, edu) • University of North Carolina, USA • University of Washington, USA • Mayo Clinic, USA • Iowa State University, USA • University of Texas, Medical Center, USA • The University of Arizona, USA • Columbia University, USA • Harvard University, USA • Johns Hopkins Medical Institutions, USA • Johns Hopkins University, USA • Medical informatics UC Davis, USA • Medical College of Wisconsin, USA • Stanford University, USA • …

  47. Users (Cont.) • Public Users (USA, non-edu) • Schering-Plough, USA • Mayo Clinic, USA • Translational Genomics Research Institute, USA • Emergint, USA • MedTopia, USA • Mitre, USA • NICHD, USA • American College of Physicians, USA • …

  48. Users (Cont.) • Public Users (international) • Vienna University of Technology, Austria • GlaxoSmithKline Research and Development, worldwide • National Institute of Hospital Administration, China • University of Manchester, UK • National Health Service, UK • The University of Western Ontario, Canada • Taipei Medical University, Taiwan • Université Paris, France • Bioinformatics Group, Japan • Seoul National University Hospital, Korea • Myong Ji University, Korea • Hôpital Charles Nicolle, France • Universitaetsklinikum Freiburg, Germany • …

  49. Annual Release Cycle • Release with UMLS Resources (Jan.) • Provide technical support and open SCRs • Create a new release baseline • Complete SCRs (Jun.) • Tests (begin) • Integrate with new LEXICON (Jul.) • Update all software components: Gui tool & examples • Internal release (Oct.) • Update all documents: apiDocs, userDocs, designDocs • Update web sites and web tools • Tests (end) • Build, pack, release, and deploy (Dec.)

  50. Tests • Unit Test (black box test): • new software components • flows components • options • Integration Test • Gui tool & Web tools • other applications • Distribution test • platforms: Linux, Unix, Window NT • Performance Test • norm • luiNorm

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